title: LNCaPHA-K205R-1-micro


title: LNCaPsh-UTR-2-micro

status: Public on May 27 2024

type: SRA

city: Shanghai

first: Renjie

last: Cai

address: 280 Mohe Road, Baoshan District

department: Department of Oncology

country: China

institute: Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China

library_source: transcriptomic

data_processing:
Unique raw fastq reads were mapped to the human transcriptome using STAR
STAR parameters:twopassMode Basic|--outSAMstrandField intronMotif|--alignSJstitchMismatchNmax 5 -1 5 5
RSEQC was used for comparison and statistics
Assembly: The transcripts in the sample are assembled by using stringtie software based on the location information file of the known transcripts on the genome
Supplementary files format and content: merged xls files include RPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: LNCaP

growth_protocol: LNCaP cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from the LNCaP stable cell lines using TRIzol (Invitrogen, CA, USA).
The total RNA was extracted using the VAHTS Universal V6 RNA seq Library Prep Kit ( Vazyme, NR604-02, Nanjing, China）for Illumina to construct the cDNA library.

tag: cell line

value: LNCaP

tag: cell type

value: Prostate cancer cells

tag: genotype

value: KHSRP knockdown


title: Pgb1.1A.0h.2

city: Winnipeg

first: Claudio

last: Stasolla

state: MB

address: 66 Dafoe Road

department: Plant Science

country: Canada

institute: University of Manitoba

data_processing:
Raw RNA-seq reads were aligned using HISAT2 (Kim et al., 2019).
Gene counts were quantified using featureCounts (Liao et al., 2014).
Assembly: Zea mays B73 RefGen_v4 (Zm-B73-GRAMENE-REFERENCE-4.0) genome assembly (Jiao et al., 2017), downloaded from the Maize Genetics and Genomics Database (MaizeGDB) (https://www.maizegdb.org).
Supplementary files format and content: Gene counts file containing raw counts (from featureCounts) of all genes for each sample

organism: Zea mays

source_name: QC of root tip

extract_protocol:
Quiescent centers (QCs) were gently separated from the weak wall junction with the proximal tissue after surgical removal of the root cap. RNA extraction from QC was carried out using the Ambion® RNaqueous® 152 micro kit.
Total RNA was submitted to Génome Québec (Montreal, Quebec) for library construction and sequencing, using NEBNext Multiplex Oligos for Illumina.

treatment_protocol: Roots of 5-day-old maize seedlings were submerged in a liquid solution [1/2 Murashige and Skoog (MS) medium] supplied with air (normoxic conditions) or 4% (v/v) oxygen/96% nitrogen (hypoxic conditions). Seedlings were collected at 6, 12, and 24 h during treatments.

tag: tissue

value: QC of root tip

tag: timepoint

tag: treatment

value: normoxic


title: E14tg2a, CtbpDKO_Dox_d18_rep2

city: Sanda

first: Yoshiyuki

last: Seki

state: hyogo

address: 1, Gakuen Uegahara

department: School of Biological and Environmental Sciences

country: Japan

institute: Kwansei Gakuin University

description:
iCt2_d18_2
iCt2_counts.txt

data_processing:
(RNA-seq) Sequence reads were trimmed using trimgalore (R-package) with option (-q 20 -j 4)
(RNA-seq) Trimed fasq files were aligned by Hisat2 to mm10 genome with defaults setting.
(RNA-seq) Read counts were extracted using R package FeatureCounts using mm10 KnownGenes.
(RRBS) Sequence reads were trimmed using trimgalore (R-package) with option (--rrbs --non_directional --paired --length 15)
(RRBS) Trimed fasq files were aligned using bismark with option (-- pbat)
(RRBS) CpG methylation was extracted using bismark_methylation_extractor
Assembly: mm10
Supplementary files format and content: tab-delimited files (RNA-seq)
Supplementary files format and content: BedGraph (RRBS)

organism: Mus musculus

growth_protocol: E14tg2a cells were maintained in GMEM with 10%FBS and LIF

extract_protocol:
Total RNAs were extracted using a PureLinkTM RNA Mini Kit (Ambion, Inc.)  Genomic DNAs were evtracted using Wizard® SV Genomic DNA Purification System 602 (Promega).
RNA-seq libraries were contructed using CollibriTM Stranded RNA library prep for ilIuminaTM Systems 582 (ThermoFisher Scientific). RRBS libraries were constructed using Premium RRBS kit V2.

value: Embryonic stem cells

value: CtbpDKO

tag: time


title: Unablated rgc:ntr day 8

city: Baltimore

first: Kevin

last: Emmerich

state: Maryland

address: 1800 Orleans St

department: Ophthalmology

country: USA

institute: Johns Hopkins University

description:
TH103
Barcode start 24_48, end with -3
RGC_24+48h_features.tsv.gz
RGC_24+48h_matrix.mtx.gz
RGC_24+48h_barcodes.tsv.gz

library_source: transcriptomic single cell

data_processing:
scRNAseq: Raw reads were mapped to the Danio rerio GRCz10 using Cell Ranger v7.0 from 10x genomics. Aligned genomic reads were then read into the published Seurat pipeline (v4.3.0.1) and quality control was performed by removing any cells with <200 detected genes or 1000 UMIs, and genes detected in fewer than 3 cells per experiment. Clustering steps were performed using steps from the pbmc Seurat tutorial available online. Briefly, the top 2,000 variable genes were identified and used to identify principal components (PCs) of the data. The top 30 PCs were used to produce a UMAP and clusters were annotated with known zebrafish marker genes. Differentially expressed genes (DEGs) were identified using the FindAllMarkers function between each control and ablation timepoint in each retinal cell cluster (minimum log2 foldchange cutoff of 0.25).
scMultiomeseq: RNA expression data was processed as above. Peak calling from single nuclei ATAC-seq reads was performed using MACS2 in the ArchR package (v1.0.2). ATAC seq data was then processed using the pbmc scATAC-seq workflow with the Signac (v1.10.0) and Seurat (v4.3.0.1) packages for quality control, normalization and producing an integrated UMAP. Differential expression and accessibility was then calculated for both gene RNA expression and chromatin peak accessibility. Next, the ChromVar package (v1.18.0) was used to identify differentially accessible transcription factor motifs between wildtype and ascl1a mutant cells.
Assembly: GRCz11
Supplementary files format and content: Cellular expression data varies in format either as h5 standalone files or barcodes, features and matrix files to be used together. ATAC data is available as standalone fragment.tsv files

organism: Danio rerio

source_name: Eye

extract_protocol:
scRNAseq: 40-60 eyes were dissected from sibling fish and subsequently placed in 20 U/ml papain (10 eyes per 1 ml) (Worthington), and incubated at 28°C for 30 min with gentle agitation. Cells were pelleted and resuspended in PBS containing 0.1 mg/ml leupeptin (Sigma-Aldrich) and 10 U/ml DNaseI (Roche). Cells were filtered through a 70-μm filter (Miltenyi Biotec), kept on ice until 10X genomics processing. scMultiomeseq: 40-60 eyes were dissected and flash-frozen in dry ice for ~15min before being transferred to a -80 C freezer for storage. Nuclei were extracted from frozen retinal tissues according to 10xMultiome ATAC + Gene Expression (GEX) protocol (CGOOO338). Briefly, frozen retinal tissues were lysed in ice-cold 500ml of 0.1X Lysis buffer using a pestle and incubated on ice for 6 min totally. Nuclei were centrifuged, washed 3 times and resuspended in 10xMultiome nuclei buffer at a concentration of ~3000-5000 nuclei/ml and kept on ice until 10x genomics processing.
Library preparation was then performed according to 10x genomics protocols.

value: Eye

tag: transgenic line

value: no mtz


title: LNCaPsh-UTR-1-micro


title: E14tg2a, CtbpDKO_Dox_d12_rep2

description:
iCt2_d12_2
iCt2_counts.txt


title: E14tg2a, CtbpDKO_Dox_d12_rep1

description:
iCt2_d12_1
iCt2_counts.txt


title: Ablated rod:ntr day 7 48h mtz, replicate 2

value: mtz


title: Unablated rod:ntr day 7, replicate 2


title: LNCaPHA-WT-2-micro

value: KHSRP knockdown-reapplied HA-KHSRP-WT


title: Pgb1.1S.12h.3

value: hypoxic


title: Pgb1.1A.0h.1


title: Ablated rod:ntr day 7 48h mtz, replicate 1


title: Unablated rgc:ntr day 7

description:
TH110
Barcode start 24_48, end with -1
RGC_24+48h_features.tsv.gz
RGC_24+48h_matrix.mtx.gz
RGC_24+48h_barcodes.tsv.gz


title: Pgb1.1A.12h.1


title: Pgb1.1S.12h.2


title: E14tg2a, CtbpDKO_Dox_d9_rep2

description:
iCt2_d9_2
iCt2_counts.txt


title: Unablated rod:ntr day 7, replicate 1


title: E14tg2a, CtbpDKO_Dox_d9_rep1

description:
iCt2_d9_1
iCt2_counts.txt


title: Pgb1.1S.12h.1


title: LNCaPHA_K205R_3


title: E14tg2a, CtbpDKO_Dox_d18_rep1

description:
iCt2_d18_1
iCt2_counts.txt


title: E14tg2a, CtbpDKO_Dox_d3_rep2

description:
iCt2_d3_2
iCt2_counts.txt


title: Pgb1.1S.0h.3


title: LNCaPHA_K205R_2


title: L. albus 20 min 10 mM sucrose  replicate 3

city: Hayward

first: Claudia

last: Uhde-Stone

state: CA

address: 25800 Carlos Bee Blvd

department: Biological Sciences

institute: California State University, East Bay

description: Oxford Nanopore

data_processing:
Equal concentration of the four cDNA libraries for each biological replication were pooled and sequenced on three separate MinION FLO-MIN106 flow cells (Oxford Nanopore Technology, ONT), using a MinION MK1C running Minknow v20.06.5 and guppy v4.09. Basecalling was performed during the run using the fast-basecalling algorithm with a Q score cutoff >7.
Demultiplexed sequencing reads in fastq format were transferred from the Mk1C device to a PC with Epi2me installed. The data was analyzed using the Epi2me wf-transcriptomes workflow version 1.1. available at https://github.com/epi2me-labs/wf-transcriptomes. Resulting read data was analyzed for differential expression using DESeq2 (time course option).
Assembly: CNRS_Lalb_1.0/GCA_009771035.1 assembly
Supplementary files format and content: csv file containing CPM (counts per million) results for each sample (CPM_genes_Lupinus_albus_sucrose.csv)
Supplementary files format and content: csv file containing DESeq2 data for 10 min (t10), 15 min (t15) and 20 min (t20) of sucrose treatment (DESeq2_all_genes_t10-t15-t20_annotated.csv)

molecule: polyA RNA

organism: Lupinus albus

source_name: 5-6 cm root sections with tip

growth_protocol: White lupin (Lupinus albus cv. Amiga) seeds were sterilized by shaking for 3 minutes in 10% bleach, followed by several rinses with sterile water. Sterile seeds were then spread out on sterile petri dishes (10-20 seeds per dish) and covered about halfway with sterile water to germinate at room temperature in the dark for 3-4 days. Once the radicles reached a length of 2-3 cm, the seedlings were transferred to containers filled with 850 ml of Hoagland solution, which was changed about every 4 days. The temperature of the growth chamber was maintained at ~21°C with a light cycle of 16 hours and a dark cycle of 8 hours.

extract_protocol:
RNA from white lupin samples was isolated following the protocol for “Purification of Total RNA from Plant Cells and Tissues, and Filamentous fungi” from RNasy Plant Mini kit (Qiagen). The Qubit 4 Fluorometer in conjunction with an RNA-High Sensitivity assay was used to quantify the samples. In addition, the RNA IQ assay was used to determine the RNA integrity number (RIN). This RIN is based on the ratio of large and/or structured RNA to small RNA in the sample. Only samples with RIN of 8 or higher were used for RNA sequencing.
Using the PCR-cDNA sequencing-barcoding (SQK-PCB111) kit of Oxford Nanopore Technologies, the extracted RNA was converted into cDNA and uniquely barcoded, following the manufacturer’s instructions.

treatment_protocol: For treatment, the plant roots of selected pots were exposed to sucrose by adding 8.5 ml of 1 M sucrose (prepared in Hoagland solution) directly to the hydroponic solution, for a final concentration of 10 mM sucrose. Harvesting was done after exposing the plants to sucrose for different periods: 0 minutes (control), 10 minutes, 15 minutes and 20 minutes. All time points were done in 3 biological replications (3 plants each). For harvesting, about 100 mg of the root tip sections with a length of about 5 cm were harvested in liquid nitrogen from each plant and stored immediately at -80 deg C

value: 5-6 cm root sections with tip

value: wildtype

value: 20 min 10 mM sucrose


title: L. albus 20 min 10 mM sucrose  replicate 2

description: Oxford Nanopore


title: LNCaPHA-WT-3-micro


title: LNCaPHA_K205R_1


title: E14tg2a, CtbpDKO_Dox_d3_rep1

description:
iCt2_d3_1
iCt2_counts.txt


title: Pgb1.1S.0h.2


title: L. albus 20 min 10 mM sucrose  replicate 1

description: Oxford Nanopore


title: E14tg2a, CtbpDKO_Dox_d0_rep2

description:
iCt2_d0_2
iCt2_counts.txt


title: WT.12hr.3

value: WT


title: E14tg2a, CtbpDKO_Dox_d0_rep1

description:
iCt2_d0_1
iCt2_counts.txt


title: LNCaPHA_WT_2


title: LNCaPHA_WT_1


title: Pgb1.1S.0h.1


title: E14tg2a, Dppa2_DuxTKO_rep1

description:
DKO_Dppa2_KO_1
WT_DKO_Dux_Dppa2_counts.txt


title: LNCaPHA_WT_3


title: LNCaPHA-WT-1-micro


title: E14tg2a, Dppa2KO_rep2

description:
Dppa2_KO_2
WT_DKO_Dux_Dppa2_counts.txt


title: LNCaPVECTOR_2


title: L. albus 10 min 10 mM sucrose  replicate 3

description: Oxford Nanopore

value: 10 min 10 mM sucrose


title: L. albus 10 min 10 mM sucrose  replicate 2

description: Oxford Nanopore


title: L. albus 15 min 10 mM sucrose  replicate 2

description: Oxford Nanopore

value: 15 min 10 mM sucrose


title: E14tg2a, Dppa2_DuxTKO_rep2

description:
DKO_Dppa2_KO_2
WT_DKO_Dux_Dppa2_counts.txt


title: WT.12hr.2


title: WT.12hr.1


title: L. albus 15 min 10 mM sucrose  replicate 1

description: Oxford Nanopore


title: heart ventricle, cJ4

city: Charleston

first: Henry

last: Sucov

state: SC

address: 173 Ashley Ave

institute: Medical Univ. South Carolina

data_processing:
Normalized read counts (generated by BGI) were used to calculate fold-change.
Assembly: mm10
Supplementary files format and content: Excel spreadsheet represents Normalized read counts

source_name: heart ventricle

extract_protocol:
RNA was extracted in Trizol (Invitrogen) with homogenization, purification was then performed using the RNeasy kit (Qiagen). 4 separate samples of RNA from BALB/cJ and 3 from BALB/cByJ passed RNA quality assessment using a BioAnalyzer.
Samples were sent to BGI Genomics for library preparation and sequencing.

value: heart ventricle


title: LNCaPVECTOR_3

value: LNCaP

value: Prostate cancer cells


title: WT.0h.3

value: QC of root tip

value: normoxic


title: E14tg2a, Dppa2KO_rep1

description:
Dppa2_KO_1
WT_DKO_Dux_Dppa2_counts.txt

value: Embryonic stem cells


title: WT.0h.2


title: L. albus 15 min 10 mM sucrose  replicate 3

description: Oxford Nanopore


title: LNCaPVECTOR_1


title: E14tg2a, DuxKO_rep2

description:
Dux_KO_2
WT_DKO_Dux_Dppa2_counts.txt

value: DuxKO


title: L. albus 10 min 10 mM sucrose  replicate 1

description: Oxford Nanopore


title: E14tg2a, Ctbp_DuxTKO_rep2

description:
DKO_Dux_KO_2
WT_DKO_Dux_Dppa2_counts.txt


title: WT.0h.1


title: L. albus no sucrose (control) replicate 3

description: Oxford Nanopore

value: control


title: E14tg2a, DuxKO_rep1

description:
Dux_KO_1
WT_DKO_Dux_Dppa2_counts.txt


title: heart ventricle, cJ1


title: E14tg2a, Ctbp_DuxTKO_rep1

description:
DKO_Dux_KO_1
WT_DKO_Dux_Dppa2_counts.txt


title: CH_DEL-CTD_rep2

city: San Diego

first: Yajing

last: Hao

address: George Palade Laboratories 9500 Gilman Drive, Room 217

department: Dept. of Cellular and Molecular Medicine

institute: University of California, San Diego

data_processing:
After obtaining raw RNA-Seq data, we first used Trimmomatic to perform sliding window trimming, cutting the average quality once within the 4-bp window falling below 20 and removing the trimmed read if it had a length less than 38. SortMeRNA (Kopylova et al., 2012) was used to filter ribosomal RNAs with default parameters. We mapped the filtered reads to the genome (genome version hg38) using STAR (Dobin et al., 2013) with parameters --outFilterScoreMinOverLread 0.1, --outFilterMatchNminOverLread 0.1, --outFilterMismatchNmax 4 and --outFilterMultimapNmax 8.
After obtaining the mapping files, we removed the duplicate reads using Picard (http://broadinstitute.github.io/picard/) with parameters MarkDuplicates and REMOVE_DUPLICATES = true. We calculated the gene read counts using FeatureCounts (Liao et al., 2014) and converted them to FPKM using the edgeR (Robinson et al., 2010) package in R language. The bigwig files of each RNA-Seq data set from the sense strand and antisense strand were obtained using bamCoverage from DeepTools with a parameter --binSize 1, --ignoreDuplicates, –minMappingQuality 255 and –normalizeUsing CPM.
For the analysis of relative gene abundance and reads signals in different samples, we constructed an in-house reference file by combing the genome assembly hg38 with our in-house spike-in sequence ( transcribed EGFP and FireFly luciferase RNA). The RNA-seq data of each fraction were mapped to the in-house reference and the ratio of reads that mapped to spike-in was also calculated ((reads mapped to spike-in)/(total mappable reads)). The FPKM value of each gene and the bigwig file signals was further normalized by the corresponding ratio of spike-in. We constructed the new Exon and intron annotation files based on the latest ReSeq gene annotation downloaded from UCSC. The SPI value and 3SS ratio were calculated as previously described (Herzel and Neugebauer, 2015).
Genome_build: hg38

source_name: HeLa S3 cell

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS and 1 x penicillin-streptomycin, at 37 C in a 5% of CO2 incubator. Cells were negative for mycoplasma (tested every three months).

extract_protocol: Each RNA was extracted using Trizol reagent and coupled with Direct-zol RNA Miniprep kit according to the manufacturer’s instructions.

treatment_protocol: The cell fractionation was performed as previously described, with additional modifications. Briefly, 5 x 106 cells were gently trypsinized and collected by centrifugation. the cell pellets were rinsed twice with ice-cold 1 x PBS and then were lysed by ice-cold CE buffer (10 mM HEPES [pH 7.5], 0.1 % NP-40, 1 mM EDTA, 1 mM DTT, 60 mM KCl and 340 mM Sucrose) for 5 min on ice. The supernatant (cytoplasmic fraction) was collected by centrifugation. the nuclei pellets were gently rinsed with ice-cold 1 x PBS/1 mM EDTA then gently resuspended in ice-cold glycerol buffer (20 mM Tris-HCl [pH 7.5], 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT and 50% glycerol). Gently mix with equal volume of nuclei lysis buffer (10 mM HEPES [pH 7.5], 1.0% NP-40, 0.2 mM EDTA, 1 mM DTT, 7.5 mM MgCl2, 300 mM NaCl and 1 M urea) and incubated on ice for 3 min, then collect the supernatant (nucleoplasm fraction) by centrifugation. the chromatin pellets were gently rinsed twice with ice-cold 1 x PBS/1 mM EDTA and then dissolved with TRIzol reagents (Invitrogen) for extracting chromatin-associated RNA. The purified chromatin-associated RNA was used for RNA-seq library preparation. RNA-seq libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes. Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. The libraries were multiplexed and sequenced with 100 bp paired end (PE100) to a depth of approximately 30 million reads per library on an Illumina NovaSeq 6000.

tag: sample type

value: CTD truncated RBP1


title: L. albus no sucrose (control) replicate 2

description: Oxford Nanopore


title: heart ventricle, cJ3


title: LNCaPsh_UTR_1

value: KHSRP knockdown


title: LNCaPsh_UTR_2


title: CH_DEL-CTD_rep1


title: L. albus no sucrose (control) replicate 1

description: Oxford Nanopore


title: heart ventricle, cJ2


title: LNCaPsh_UTR_3


title: CH_WT-CTD_rep2

value: full-length RBP1


title: E14tg2a, WT_rep2

description:
WT_2
WT_DKO_Dux_Dppa2_counts.txt


title: OB-wMel, Malpighian tubule, 2 dpi

city: Toyoake

first: Takahiro

last: Shirozu

state: Aichi

address: 1-98 Dengakugakubo, Kutsukake-cho

institute: Fujita Health University

data_processing:
CLC Genomics Workbench ver.11.0.1
Assembly: Aedes-aegypti-LVP_AGWG_TRANSCRIPTS_AaegL5.2 from VectorBase
Supplementary files format and content: Total counts, RPKM, TPM, CPM and comparison data of RPKM between each strain

organism: Aedes aegypti

source_name: LVP-OB-wMel

extract_protocol:
Total RNA was extracted from pooled Malpighian tubules (n > 10) derived from dissected mosquitoes at 2 dpi using PureLink™ RNA Mini Kit (Thermo Fisher Scientific).
Non-directional RNA-seq libraries were prepared in-house (Novogene).

treatment_protocol: Approximately seven days after emergence, the mosquitoes were starved for 12 h and artificially fed D. immitis-infected blood at a concentration of 6-12 microfilaria/μL.

value: Malpighian tubule

value: Wolbachia and Dirofilaria immitis infection


title: E14tg2a, CtbpDKO_rep1

description:
DKO_1
WT_DKO_Dux_Dppa2_counts.txt

value: CtbpDKO


title: heart ventricle, cByJ3

value: BALB/cByJ


title: MGYP2, Malpighian tubule, 2 dpi


title: heart ventricle, cByJ1


title: heart ventricle, cByJ2


title: MGYP2.tet, Malpighian tubule, 2 dpi

value: Dirofilaria immitis infection


title: CH_WT-CTD_rep1


title: E14tg2a, WT_rep1

description:
WT_1
WT_DKO_Dux_Dppa2_counts.txt

value: WT


title: acute lymphoblastic leukemia M168

status: Public on May 26 2024

type: genomic

city: Lublin

first: Borys

last: Styka

state: Lubelskie

address: ul. Prof. Antoniego Gębali 6

department: Genetic diagnostics department

country: Poland

institute: University Children's Hospital in Lublin

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.

label: biotin

molecule: genomic DNA

source_name: blast cells, bone marrow

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: disease

value: acute lymphoblastic leukemia

tag: age


title: acute lymphoblastic leukemia M170


title: acute lymphoblastic leukemia M171


title: acute lymphoblastic leukemia M173


title: OB, Malpighian tubule, 2 dpi

source_name: LVP-OB


title: acute lymphoblastic leukemia M174


title: acute lymphoblastic leukemia M163


title: acute lymphoblastic leukemia M161


title: acute lymphoblastic leukemia M158


title: E14tg2a, CtbpDKO_rep2

description:
DKO_2
WT_DKO_Dux_Dppa2_counts.txt


title: acute lymphoblastic leukemia M169


title: acute lymphoblastic leukemia M154


title: acute lymphoblastic leukemia M152


title: acute lymphoblastic leukemia M172


title: acute lymphoblastic leukemia M166


title: acute lymphoblastic leukemia M167


title: acute lymphoblastic leukemia M157


title: acute lymphoblastic leukemia M164


title: acute lymphoblastic leukemia M160


title: acute lymphoblastic leukemia M162


title: acute lymphoblastic leukemia M156


title: acute lymphoblastic leukemia M153


title: acute lymphoblastic leukemia M150


title: acute lymphoblastic leukemia M147


title: acute lymphoblastic leukemia M144


title: acute lymphoblastic leukemia M165


title: acute lymphoblastic leukemia M148


title: acute lymphoblastic leukemia M149


title: acute lymphoblastic leukemia M139


title: acute lymphoblastic leukemia M146


title: acute lymphoblastic leukemia M138


title: acute lymphoblastic leukemia M143


title: acute lymphoblastic leukemia M145


title: acute lymphoblastic leukemia M142


title: acute lymphoblastic leukemia M140


title: acute lymphoblastic leukemia M141


title: acute lymphoblastic leukemia M136


title: acute lymphoblastic leukemia M135


title: acute lymphoblastic leukemia M155


title: acute lymphoblastic leukemia M133


title: acute lymphoblastic leukemia M134


title: acute lymphoblastic leukemia M129


title: acute lymphoblastic leukemia M131


title: acute lymphoblastic leukemia M151


title: acute lymphoblastic leukemia M130


title: acute lymphoblastic leukemia M128


title: acute lymphoblastic leukemia M126


title: acute lymphoblastic leukemia M127


title: acute lymphoblastic leukemia M132


title: acute lymphoblastic leukemia M125


title: acute lymphoblastic leukemia M123


title: acute lymphoblastic leukemia M122


title: acute lymphoblastic leukemia M121


title: acute lymphoblastic leukemia M120


title: acute lymphoblastic leukemia M118


title: acute lymphoblastic leukemia M119


title: acute lymphoblastic leukemia M137


title: acute lymphoblastic leukemia M115


title: acute lymphoblastic leukemia M124


title: acute lymphoblastic leukemia M116


title: acute lymphoblastic leukemia M117


title: acute lymphoblastic leukemia M113


title: acute lymphoblastic leukemia M112


title: acute lymphoblastic leukemia M111


title: acute lymphoblastic leukemia M110


title: acute lymphoblastic leukemia M109


title: acute lymphoblastic leukemia M107


title: acute lymphoblastic leukemia M108


title: acute lymphoblastic leukemia M106


title: acute lymphoblastic leukemia M105


title: acute lymphoblastic leukemia M104


title: acute lymphoblastic leukemia M103


title: acute lymphoblastic leukemia M100


title: acute lymphoblastic leukemia M99


title: acute lymphoblastic leukemia M98


title: acute lymphoblastic leukemia M96


title: acute lymphoblastic leukemia M102


title: acute lymphoblastic leukemia M94


title: acute lymphoblastic leukemia M97


title: acute lymphoblastic leukemia M95


title: acute lymphoblastic leukemia M92


title: acute lymphoblastic leukemia M114


title: acute lymphoblastic leukemia M93


title: acute lymphoblastic leukemia M90


title: acute lymphoblastic leukemia M91


title: acute lymphoblastic leukemia M88


title: acute lymphoblastic leukemia M89


title: acute lymphoblastic leukemia M101


title: acute lymphoblastic leukemia M86


title: acute lymphoblastic leukemia M84


title: plasmid DNA fragments, amplified, library after sorting in the second round

city: Tianjin

first: Lixia

last: Fang

address: 135 Yaguan Road, Jinnan District

institute: Tianjin University

library_source: other

data_processing:
The original data of sequencing results were subjected to image Base calling by using CASAVA 1.8.2, and the quality was preliminarily analyzed, getting the Pass Filter Data. The sequencing data was optimized by using Cutadapt 1.9.1, removing the primers and adapter, the bases with the quality score below 20 at both ends, and the reads with N base ratio more than 10%. Clean Reads are merged to generate a complete sequence by using Pandaseq 2.7 according to the overlap regions between Read1 and Read2. The target sequence is captured according to the 10 nt of upstream and downstream of the target sequence. The merged sequences are aligned to the reference sequence by using BWA software, the section on the alignment is extracted, and abundance information is counted.
Assembly: GCF_000005845.2_ASM584v2
Supplementary files format and content: Excel file-the reads of sgRNAs in the first round of screening
Supplementary files format and content: Excel file-the reads of sgRNAs in the second round of screening
Library strategy: Amplicon sequencing

molecule: other

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Escherichia coli

growth_protocol: The transformed cells were incubated in LB broth (1:4, v/v) for 1.5 h at 37 °C to recover and washed with fresh M9 medium with the corresponding antibiotic (1:1, v/v) once. The resulting culture was incubated with 100 ml of modified M9 medium (with chloramphenicol and ampicillin) in 500 ml flasks with shaking at 30℃ and 250 rpm. The cultures were induced with 1 mM IPTG at an OD600 of about 1.0 and allowed to grow for an additional 40 h to sample the cell library (before sorting, BS). The cell library (before sorting, BS) was dyed with Nile red and sorted by FACS, obtaining the cell library after sorting (AS).

extract_protocol:
Plasmid extraction was performed using the TIANprep Mini Plasmid Kit (Tiangen, China). The plasmids were used as templates for PCR to amplify the N20 region of library sgRNAs. The PCR fragment was purified using the TIANquick Midi purification Kit (Tiangen, China).
For each sample, the purified PCR products were treated with End Prep Enzyme Mix for end repairing, 5’ phosphorylation, and dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Adaptor-ligated DNA was then performed using DNA Clean Beads. A second PCR reaction was carried out with P5 and P7 primers carrying sequences which can anneal with flowcell to perform bridge PCR and index allowing for multiplexing. The products were purified by beads and then qualified. The final libraries were sequenced via the Illumina NovaSeq 6000 platform using a 2 × 150 paired-end configuration.

value: Escherichia coli


title: plasmid DNA fragments, amplified, library after sorting in the first round


title: plasmid DNA fragments, amplified, library before sorting in the second round


title: plasmid DNA fragments, amplified, the transformed library in the first round


title: Recanalized_D7_rep1

city: Chongqing

first: Wen

last: Zeng

address: Gaotanyan street

department: Department of Cell Biology

institute: Army Medical University

data_processing:
reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2.2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach.
Assembly: mRatBN7
Supplementary files format and content: readcount.xlsx file includes raw counts for each Sample
Supplementary files format and content: fpkm.xlsx file includes fpkm values for each Sample

organism: Rattus norvegicus

source_name: blood vessels

extract_protocol:
RNA was harvested using Trizol reagent kit, Total RNA was qualified and quantified as follows: (1) RNA purity and concentration were then examined using NanoDrop 2000; (2) RNA integrity and quantity were measured using the Agilent 2100/4200 system.
mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities.  After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library.

treatment_protocol: Rat common carotid artery thrombosis was induced by ferric chloride, vascular recanalization was achieved under the combination of sonodynamic therapy and physical-explosion therapy, and the recanalized common carotid arteries were collected after one day and one week. Normal rat common carotid artery was taken as control.

value: blood vessels

value: Recanalized

tag: time point


title: acute lymphoblastic leukemia M83


title: Recanalized_D7_rep2


title: Recanalized_D1_rep3


title: acute lymphoblastic leukemia M81


title: acute lymphoblastic leukemia M80


title: Recanalized_D1_rep2


title: acute lymphoblastic leukemia M82


title: Recanalized_D1_rep1


title: acute lymphoblastic leukemia M79


title: acute lymphoblastic leukemia M78


title: acute lymphoblastic leukemia M87


title: plasmid DNA fragments, amplified, library before sorting in the first round


title: acute lymphoblastic leukemia M77


title: acute lymphoblastic leukemia M76


title: acute lymphoblastic leukemia M75


title: acute lymphoblastic leukemia M85


title: acute lymphoblastic leukemia M74


title: acute lymphoblastic leukemia M73


title: acute lymphoblastic leukemia M72


title: acute lymphoblastic leukemia M69


title: acute lymphoblastic leukemia M70


title: K562 cells DUBR TSS mutant 2,  BBQ locus viewpoint, biol_rep 1

city: Mexico City

first: Carlos

middle: Alberto

last: Peralta-Alvarez

state: Ciudad de México

address: Circuito Exterior s/n Ciudad Universitaria, Coyoacán

department: Genética Molecular

country: Mexico

institute: Universidad Nacional Autónoma de México

library_source: genomic

data_processing:
*library strategy: 4C-seq
Pipe4C was utilized for preprocessing and analysis of all samples
hg19 reference genome was used for all aligments
deeptools multiBamSummary was used to estimate scaling factors by viewpoint to create bigwig files using bamCoverage
Assembly: hg19
Supplementary files format and content: bigwig

source_name: Bone marrow

extract_protocol:
10 million cells were crosslinked with 2% formaldehyde for 10 minutes, followed by 5-minute quenching with glycine. Cells were washed once with PBS, and then cells were incubated for 20 min in lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 0.2% Igepal) with 1x protease inhibitors. For the first digestion, three rounds of digestion were made with DpnII (NEB R0543S) at 37 C in a thermomixer at 500 RPM (100U for 4 hours, 100U overnight, and 100U for another 4 hours); the restriction enzyme was inactivated by heating to 62 C for 20 minutes while shaking at 500 rpm. Then the first ligation was made with 2000U of T4 DNA ligase (NEB M0202L) at 16 C in 7mL of Milli-Q water overnight. Samples were then phenol-chloroform extracted and ethanol precipitated, and the second digestion was performed overnight with 50U of NlaIII (NEB R0125S) or HindIII (NEB R0104S). The second ligation was performed in 5mL total with 3000 units of T4 DNA ligase (NEB M0202L).
Libraries were constructed starting from the second ligation material which was purified with SPRI beads, and it was quantified with a Qubit dsDNA Assay Kit. A first round of PCR amplification with viewpoint-specific primers  was performed with 4 x 50 µL PCR reactions with 200ng of 4C template using 16 PCR cycles and the Phusion polymerase (NEB M0530L). A second round of PCR with universal primers containing Illumina adapters was performed, and the material was purified with SPRI beads.

value: Bone marrow

value: Chronic Myelogenous Leukemia

value: DUBR TSS mutant


title: K562 cells DUBR TSS mutant 1,  BBQ locus viewpoint, biol_rep 1


title: K562 cells wild-type,  BBQ locus viewpoint, biol_rep 2

value: wild-type


title: K562 cells wild-type,  BBQ locus viewpoint, biol_rep 1


title: Control

value: health blood vessel


title: K562 cells DUBR TSS mutant 2,  BBQ locus viewpoint, biol_rep 2


title: acute lymphoblastic leukemia M67


title: DZ1503

type: RNA

city: Shijiazhuang

first: Jingjing

last: Liu

state: Hebei

address: Research Center, the Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China

institute: Hebei Medical University

description: Gene expression after transfect Vector

hyb_protocol: The labeled cRNAs were hybridized onto the microarray. After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, the raw data was normalized with the quantile algorithm. The probes detected with at least 75.0 percent in any group were chosen for further data analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 1.5 and a P value<= 0.05. Afterwards, GO analysis and KEGG analysis were applied to determine the roles of these differentially expressed mRNAs. Finally, Hierarchical Clustering was performed to display the distinguishable genes' expression pattern among samples.

source_name: control 3

label_protocol: Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

growth_protocol: The cells was cultured in Roswell Park Memorial Institute 1640 complete medium, enriched with double antibody (Gibco, Thermo Fisher Scientific, Inc.), 10% fetal bovine serum (Gibco, Thermo Fisher Scientific, Inc.), and 1% penicillin. In a sterile incubator at 37˚C with 5% CO2.

extract_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: TRIzol treats the cells

value: Transfect Vector


title: acute lymphoblastic leukemia M71


title: SY1501

description: Gene expression after transfect circJPH1

scan_protocol: The labeled cRNAs were hybridized onto the microarray. After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

source_name: experiment 1

value: Transfect circJPH1


title: SY1502

source_name: experiment 2


title: DZ1501

description: Gene expression after transfect Vector

source_name: control 1


title: DZ1502

description: Gene expression after transfect Vector

source_name: control 2


title: K562 cells DUBR TSS mutant 1,  BBQ locus viewpoint, biol_rep 2


title: acute lymphoblastic leukemia M66


title: K562 cells BBQ mutant 1,  BBQ locus viewpoint, biol_rep 1

value: BBQ mutant


title: K562 cells BBQ mutant 1,  BBQ locus viewpoint, biol_rep 2


title: acute lymphoblastic leukemia M68


title: K562 cells wild-type,  BBX TSS viewpoint, biol_rep 2


title: acute lymphoblastic leukemia M65


title: acute lymphoblastic leukemia M64


title: acute lymphoblastic leukemia M63


title: K562 cells wild-type,  BBX TSS viewpoint, biol_rep 1


title: SY1503

source_name: experiment 3


title: acute lymphoblastic leukemia M62


title: acute lymphoblastic leukemia M61


title: K562 cells DUBR TSS mutant 2,  BBX TSS viewpoint, biol_rep 2


title: K562 cells DUBR TSS mutant 1,  BBX TSS viewpoint, biol_rep 2


title: K562 cells DUBR TSS mutant 1,  BBX TSS viewpoint, biol_rep 1


title: K562 cells DUBR TSS mutant 2,  BBX TSS viewpoint, biol_rep 1


title: acute lymphoblastic leukemia M56


title: acute lymphoblastic leukemia M60


title: acute lymphoblastic leukemia M55


title: acute lymphoblastic leukemia M59


title: K562 cells, BBQ mutant 2, biol_rep 1

data_processing:
Raw sequencing files were trimmed for adapters and by quality parameters using TrimGalore!
Aligment to hg19 reference genome were done using Bowtie2
Raw counts from reference annotation genes were obtained with FeatureCounts with parameters "- p", "-t exon", and "-g gene_id"
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include raw counts for each Sample

extract_protocol:
RNA was harvested from confluent culture boxes using TRIzol reagent (Thermofisher) according to manufacturer instructions, 2 ug of RNA was utilized for library preparation.
Libraries were constructed using TruSeq RNA Library Prep Kit (Illumina) according to manufacturer protocol

value: DUBR/LINC00882 promoter monoallelic mutant


title: K562 cells, BBQ mutant 2, biol_rep 3


title: K562 cells, BBQ mutant 2, biol_rep 2


title: acute lymphoblastic leukemia M57


title: acute lymphoblastic leukemia M58


title: acute lymphoblastic leukemia M54


title: K562 cells BBQ mutant 1,  BBX TSS viewpoint, biol_rep 2


title: acute lymphoblastic leukemia M53


title: acute lymphoblastic leukemia M52


title: acute lymphoblastic leukemia M51


title: K562 cells, BBQ mutant 1, biol_rep 2


title: K562 cells, BBQ mutant 1, biol_rep 3


title: K562 cells, Wild-type control, biol_rep 2

value: Wild-type


title: acute lymphoblastic leukemia M49


title: K562 cells, Wild-type control, biol_rep 3


title: acute lymphoblastic leukemia M48


title: K562 cells, Wild-type control, biol_rep 1


title: miRNA AX8

first: Yongzhi

last: Wang

state: Shanghai

address: Huashan Road 1954

institute: Shanghai Jiao Tong University

data_processing:
Data quality control was performed on raw RNA-sequencing results. For the mRNA and lncRNA sequencing data, we utilized the FastQC software (version 0.11.9) for initial quality checks and Cutadapt (version 4.2) software for adapter trimming. Following quality control, the sequencing reads were mapped to the mouse reference genome (Mus musculus GRCm38) using the HISAT2 software (version 2.2.1). Quantitative analysis of the RNA-Seq data was conducted using the StringTie software (version 2.1.5). The original expression profile was compared to the mouse annotation file to distinguish mRNA from lncRNA for further analysis.
For the miRNA sequencing data, quality control was performed and sequencing adapters were removed using Cutadapt software (version 4.2). After rigorous sequence filtering, target sequences within the 18 to 35 nucleotide (nt) range were selected. The distribution of these target sequences primarily fell within the 20 to 24 nt range, aligning with the typical length of microRNAs. Subsequently, the target sequences were mapped to the mouse reference genome (mm38) using Bowtie2 software (version 2.5.1). The aligned sequences were extracted and further mapped to the mouse reference microRNAs in miRbase using the Bowtie2 software (version 2.5.1). The CIRI2 software was employed for quantification and differential expression analysis of circle RNA.

source_name: liver

growth_protocol: Male C57BL/6 mice (n=45, six weeks old) were randomly assigned to three groups: the CCl4-induced liver cancer group (liver cancer group), the PTH and CCl4-treated group (treatment group), and the control group (normal control group), with 15 mice per group. The mice in the normal control group received intragastric administration of double distilled water daily and intraperitoneal injections of olive oil twice a week. The liver cancer group was treated with intragastric administration of double distilled water daily and intraperitoneal injection of CCl4 twice a week. PTH was administrated intragastrically once a day for the treatment group, and CCl4 was injected intraperitoneally twice a week. In the 22nd week, we selected six mice from each group for RNA sequencing.

extract_protocol:
We extracted RNA from the mice liver tissues following the TRIzol reagent protocol provided by the manufacturer(Sigma).
After the removal of ribosomal RNA, two sequencing libraries were generated: NEBNext RNA Library Prep Kit (from NEB, USA) was used for lncRNA, circRNA, and mRNA sequencing, while the small RNA libraries were constructed using VAHTS Small RNA Library Prep Kit for Illumina (Vazyme #NR801) following the manufacturer's recommendations, respectively. Following the manufacturer's instructions, subsequent sequencing was performed on the Illumina HiSeq 4000 platform for paired-end 150 bp sequencing of lncRNAs, circRNAs and mRNAs, and on the Illumina NovaSeq platform for paired-end 50 bp sequencing of miRNAs.

treatment_protocol: We construct two groups liver cancer mice model using CCl4, one group treated with PZH and the other not.

value: liver

value: PTH week 22


title: K562 cells BBQ mutant 1,  BBX TSS viewpoint, biol_rep 1


title: acute lymphoblastic leukemia M47


title: miRNA AX7


title: acute lymphoblastic leukemia M46


title: acute lymphoblastic leukemia M45


title: acute lymphoblastic leukemia M44


title: miRNA AX6


title: miRNA AX3


title: acute lymphoblastic leukemia M43


title: miRNA AX2


title: acute lymphoblastic leukemia M41


title: acute lymphoblastic leukemia M50


title: acute lymphoblastic leukemia M42


title: acute lymphoblastic leukemia M40


title: miRNA AX1


title: male parasites, klf4 RNAi, rep3

city: DALLAS

first: Lu

last: Zhao

state: TX

address: 6001 Forest Park Road, ND7.300

department: Pharmacology

institute: The University of Texas Southwestern Medical Center

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Schistosoma mansoni genome (v7) using STAR (v2.7.10a).
Pairwise comparisons of differential gene expression were performed with DESeq2 (1.30.1).
Assembly: Schistosoma mansoni v7
Supplementary files format and content: Excel spreadsheet (xlsx.) file containing analysis of data generated from three replicates of klf4 RNAi samples and 3 replicates of control RNAi samples. Statistical significance determined by the Wald test in DESeq2 (version 1.30.1)
Supplementary files format and content: Excel spreadsheet (xlsx.) file containing normalized counts of each sample

organism: Schistosoma mansoni

source_name: whole worm extract

growth_protocol: Adult male parasites cultured in Basch Media 169 at 37°C at 5% CO2 for 17 days

extract_protocol:
Total RNA was extracted using Trizol reagent and purified using a Zymo Direct-zol RNA miniprep kit before Illumina sequencing.
RNA libraries were prepared for sequencing using Illumina Truseq stranded mRNA library preparation kit.

treatment_protocol: Freshly perfused male parasites were treated with 30ug/mL dsRNA on D0, 1, 2, 5, 8, 11 and given fresh media on Day 14

value: whole worm extract

tag: strain

value: Puerto Rico

value: klf4 dsRNA


title: male parasites, klf4 RNAi, rep2


title: K562 cells, BBQ mutant 1, biol_rep 1


title: acute lymphoblastic leukemia M39

value: acute lymphoblastic leukemia


title: miRNA AT8

value: CCL4 week 22


title: male parasites, klf4 RNAi, rep1


title: male parasites, control RNAi, rep3

value: control dsRNA


title: acute lymphoblastic leukemia M37


title: acute lymphoblastic leukemia M36


title: miRNA AT7


title: acute lymphoblastic leukemia M35


title: miRNA AT5


title: male parasites, control RNAi, rep1


title: mNPCs derived from mES-E14TG2a, biological replicate 1

city: Amsterdam

first: Max

last: Trauernicht

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Adapter sequences and low quality reads were removed with fastp (v0.12.2). Reads were aligned to mm10 and counted in gencode v24 genes with STAR (v2.5.4a).
Assembly: mm10
Supplementary files format and content: File contains raw read counts per gene.

source_name: Neural

growth_protocol: Cells were cultured as previously published (Peric-Hupkes et al., PMID: 20513434).

extract_protocol:
1x10^6 mNPC cells were resuspended in 600 uL RLT buffer (Qiagen). RNA was extracted using RNeasy plus kit (Qiagen).
Libraries were prepared using Illumina stranded RNA Library kit following manufacturer's instructions.

value: Neural

value: mNPC

value: neural precursor cells


title: acute lymphoblastic leukemia M34


title: miRNA AT4


title: Autotetraploid jujube under 48h drought treatment (repeat 3)

city: Beijing

first: Yingyue

last: Li

address: Haidian District, Beijing

institute: Beijing Forestry University

description:
T48h-3
T48h-3_ZiziphusjujubaMill_V198-01-T24
processed data file: T48h-1,T48h-2,T48h-3.txt

data_processing:
Illumina Casava1.8 and Bcltofastq 1.8.4 software used for basecalling analysis.
Clean data were obtained after removing all adapter- and poly-Ncontaining sequences and low-quality reads from the raw data, and Q20 and Q30 values, GC content, and sequence duplication levels were then calculated. The clean reads were mapped to the Ziziphus jujuba Dongzao genome using HISAT2 software (Kim et al., 2015). Only reads with no more than one mismatch were further analyzed and annotated against the reference genome.
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated by StringTie. FPKM=cDNAs Fragments/(MappedFragment(millions)*Transcriptlength(kb)).CDNA fragments represent the number of fragments aligned to a certain transcript, i.e. the number of two terminal reads; Mapped fragments (millions) represents the total number of fragments compared to transcripts, in units of 10 ^ 6; Transcript length (KB): transcript length, in units of 10 ^ 3 bases.
Genome_build: Ziziphus jujuba cultivar:Dongzao
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample with 3 biological repeats.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Ziziphus jujuba var. spinosa

growth_protocol: More than twenty generations diploid and its autotetraploid seedlings were tissue-cultured synchronously under 16/8 h light/dark cycle at 25 ± 2 °C and 130μmolm-2s-1 illumination intensity. After tissue culture of 30 days, well-growing plants were cultured in the rooting medium for 45 days.

extract_protocol:
Leaves under control and drought treatment of 6h, 12h and 48h were sampled from diploid and the autotetraploid for RNA-seq. Total RNA was extracted from 100mg sample with plant RNA kit (Omega Biotech, China) and purified with RNase-Free DNase set. Following, RNA concentration was measured on the NanoDrop 2000 spectrophotometer (Thermo Scientific, MA), and RNA integrity was assessed using an RNA Nano 6000 Assay kit supplied with the Agilent Bioanalyzer 2100 system (Agilent Technologies, USA).
A total of 1μg RNA was used to construct cDNA library and the library concentration and insert size was respectively assessed on the Qubit2.0 (Invitrogen, USA) and Agilent Bioanalyzer 2100 system, and then the effective concentration of the library was accurately quantified through Q-PCR.

treatment_protocol: Diploids and autotetraploid plants with uniform growth were transferred to 3% Hoagland and Arnon solution (pH 6.0 ± 0.2) with dark for 3 days and light for 7 days before treatment. The nutrient solution was replaced every two days and kept sterile. Following PEG6000 was gradually applied to the seedlings to avoid osmotic shock which is 5%, 10%, 15% and finally 20% over 1-day intervals under 16/8 h light/dark cycle at 25 ± 2 °C and 130μmolm-2s-1 illumination intensity.

tag: ploidy/cultivar

value: Autotetraploid Ziziphus jujuba Mill. var. spinosa

value: leaves

value: after tissue culture of 30 days, well-growing plants were cultured in the rooting medium for 45 days

value: autotetraploid

value: 48h drought treatment


title: miRNA AT1


title: acute lymphoblastic leukemia M32


title: miRNA AT2


title: Autotetraploid jujube under 48h drought treatment (repeat 1)

description:
T48h-1
T48h-1_ZiziphusjujubaMill_V198-01-T22
processed data file: T48h-1,T48h-2,T48h-3.txt


title: Autotetraploid jujube under 48h drought treatment (repeat 2)

description:
T48h-2
T48h-2_ZiziphusjujubaMill_V198-01-T23
processed data file: T48h-1,T48h-2,T48h-3.txt


title: miRNA AC8

value: water week 22


title: acute lymphoblastic leukemia M30


title: 29.4 5xFAD Sham

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

description:
10X Genomics
294bLELE143RH-HetRH

data_processing:
The FASTQ demultiplexing, cell barcode processing, genome alignment, and gene expression quantification was performed using the 10X Genomics CellRanger software v6.0.2 (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: barcodes files are text file lists of all the cell barcodes identified per sample
Supplementary files format and content: features files are tab seperated text files of all the genes analyzed in the experiment
Supplementary files format and content: matrix files are a tab seperated text file that quantifies the expression of each gene for each barcode

source_name: Hippocampus

extract_protocol:
Brain dissection and hippocampal cell dissociation were performed in 6 separate experiments. In each experiment we utilized the contralateral hemisphere as an internal control for each biological replicate. No randomization or blinding were performed during sample collection as no comparisons of different conditions were performed. For single-cell dissociation of the hippocampus, the mice were anesthetized with isoflurane, and the brain was quickly removed and transferred into ice-cold Hibernate A medium under a dissection microscope and then subjected to tissue dissociation. Hippocampal tissues were enzymatically digested using the Adult Brain Dissociation kit and mechanically disrupted with the gentleMCAS Dissociator according to the manufacturer’s instructions. Briefly, tissue from each sample as loaded into a C tube with Enzyme 1 and 2. Tissue was subsequently dissociated on the gentleMACS Octo Dissociator with Heaters for 20-100 mg tissue. Following dissociation, samples were strained through a 70mm filter with dPBS and centrifuged at 300g x 10 min at 4oC. The supernatant was removed, and the tissue was resuspended in an appropriate amount of dPBS (<400mg, 1550 mL). Next, Debris Removal Solution was added (<400mg, 450mL) and overlaid with dPBS being careful not to disrupt the lower layer and centrifuged at 3000g x 10min at 4oC.  After removing the top two layers and adding fresh dPBS, the cells were spun at 1000g x 10 min and re-suspended in 0.2 ml of dPBS with 0.05% BSA. A 15-μl cell suspension was stained with trypan blue, and the live cells were counted. In all samples, cells were greater than 90% viable. During the entire procedure, the tissues and cells were kept in ice-cold solutions.
The cell suspension was diluted with DPBS containing 0.05% BSA for single-cell capture. Cell suspensions were assessed using the Nexcelom Cellometer K2. The suspensions were prepped following 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide.  Briefly, cells are partitioned into nanoliter gel beads-in-emulsion (GEMs). A pool of ~3,500,000 10x Genomics barcodes are used to index each individual cell separately and uniquely. Libraries are then created and sequenced on the Illumina Novaseq 6000, with 10x barcodes used to assign reads back to individual partitions, and therefore, to each individual cell. More than 10,000 single-cell events derived from hippocampal cells of mice were captured for recovery.

treatment_protocol: 5xFAD or WT mice were subject to a transient 60 minute stroke via the middle cerebral artery occlusion (MCAO). The ipsilateral hemisphere was used as the stroke side for hippocampal isolation. The contralateral hemisphere was used as an interal control and utilized as the sham treatment group to maximize biological material.

value: Hippocampus

tag: hemisphere

value: contralateral

tag: Sex

value: Female

value: 12 months old

value: Sham


title: 28.5 5xFAD MCAO

description:
10X Genomics
285aRE135LH-HetLH

value: ipsilateral

value: Male

value: MCAO


title: Autotetraploid jujube under 12h drought treatment (repeat 2)

description:
T12h-2
T12h-2_ZiziphusjujubaMill_V198-01-T17
processed data file: T12h-1,T12h-2,T12h-3.txt

value: 12h drought treatment


title: 29.4 5xFAD MCAO

description:
10X Genomics
294bLELE143LH-HetLH


title: acute lymphoblastic leukemia M29

value: acute lymphoblastic leukemia


title: mNPCs derived from mES-E14TG2a, biological replicate 2

value: Neural

value: mNPC

value: neural precursor cells


title: 28.5 5xFAD Sham

description:
10X Genomics
285aRE135RH-HetRH


title: acute lymphoblastic leukemia M31


title: miRNA AC4

city: Shanghai

value: liver


title: miRNA AC5


title: 28.2 WT MCAO

description:
10X Genomics
282bRE132LH-1117LH

value: WT


title: male parasites, control RNAi, rep2

value: whole worm extract

value: Puerto Rico

value: control dsRNA


title: Autotetraploid jujube under 12h drought treatment (repeat 1)

description:
T12h-1
T12h-1_ZiziphusjujubaMill_V198-01-T16
processed data file: T12h-1,T12h-2,T12h-3.txt

value: Autotetraploid Ziziphus jujuba Mill. var. spinosa

value: leaves

value: after tissue culture of 30 days, well-growing plants were cultured in the rooting medium for 45 days

value: autotetraploid


title: acute lymphoblastic leukemia M28


title: acute lymphoblastic leukemia M33


title: Autotetraploid jujube under 6h drought treatment (repeat 3)

description:
T6h-3
T6h-3_ZiziphusjujubaMill_V198-01-T12
processed data file: T6h-1,T6h-2,T6h-3.txt

value: 6h drought treatment


title: acute lymphoblastic leukemia M27


title: miRNA AC3

value: water week 22


title: Autotetraploid jujube under 12h drought treatment (repeat 3)

description:
T12h-3
T12h-3_ZiziphusjujubaMill_V198-01-T18
processed data file: T12h-1,T12h-2,T12h-3.txt


title: 28.8 WT MCAO

description:
10X Genomics
288aLERE139LH-WTLH

value: Hippocampus

value: ipsilateral

value: Male

value: 12 months old

value: MCAO


title: acute lymphoblastic leukemia M26

value: acute lymphoblastic leukemia


title: Autotetraploid jujube under 6h drought treatment (repeat 2)

description:
T6h-2
T6h-2_ZiziphusjujubaMill_V198-01-T11
processed data file: T6h-1,T6h-2,T6h-3.txt


title: 28.8 WT Sham

description:
10X Genomics
288aLERE139RH-WTRH

value: contralateral

value: Sham


title: 25.4 WT MCAO

description:
10X Genomics
254bRE129LH-WTLH

value: Female

value: WT


title: acute lymphoblastic leukemia M25


title: 25.4 WT Sham

description:
10X Genomics
254bRE129RH-WTRH


title: acute lymphoblastic leukemia M24


title: Autotetraploid jujube under control environment (repeat 2)

description:
TCK-2
TCK-2_ZiziphusjujubaMill_V198-01-T05
processed data file: TCK-1,TCK-2,TCK-3.txt

value: control environment


title: Mouse,PT-circSCMH1,rep3

city: Nanjing

first: Yu

state: Jiangsu

address: Dingjiaqiao 87

department: Department of Pharmacology

institute: Southeast University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the mus musculus（ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/） reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: brain

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: brain

value: photothrombotic (PT) stroke model treated with RVG-EVs


title: Autotetraploid jujube under control environment (repeat 3)

description:
TCK-3
TCK-3_ZiziphusjujubaMill_V198-01-T06
processed data file: TCK-1,TCK-2,TCK-3.txt

value: Autotetraploid Ziziphus jujuba Mill. var. spinosa

value: leaves

value: after tissue culture of 30 days, well-growing plants were cultured in the rooting medium for 45 days


title: Mouse,PT-circSCMH1,rep2


title: Autotetraploid jujube under 6h drought treatment (repeat 1)

description:
T6h-1
T6h-1_ZiziphusjujubaMill_V198-01-T10
processed data file: T6h-1,T6h-2,T6h-3.txt

value: autotetraploid

value: 6h drought treatment


title: acute lymphoblastic leukemia M22


title: acute lymphoblastic leukemia M21


title: Autotetraploid jujube under control environment (repeat 1)

description:
TCK-1
TCK-1_ZiziphusjujubaMill_V198-01-T04
processed data file: TCK-1,TCK-2,TCK-3.txt


title: acute lymphoblastic leukemia M23


title: 28.2 WT Sham

description:
10X Genomics
282bRE132RH-1117RH

value: Hippocampus

value: ipsilateral


title: Mouse,PT-circSCMH1,rep1


title: Diploid jujube under 48h drought treatment (repeat 3)

description:
D48h-3
D48h-3_ZiziphusjujubaMill_V198-01-T21
processed data file: D48h-1,D48h-2,D48h-3.txt

value: Ziziphus jujuba Mill. var. spinosa

value: wild type

value: 48h drought treatment


title: Diploid jujube under 48h drought treatment (repeat 2)

description:
D48h-2
D48h-2_ZiziphusjujubaMill_V198-01-T20
processed data file: D48h-1,D48h-2,D48h-3.txt


title: Mouse,PT-Vector,rep3


title: Mouse,PT-Vector,rep2


title: Diploid jujube under 48h drought treatment (repeat 1)

description:
D48h-1
D48h-1_ZiziphusjujubaMill_V198-01-T19
processed data file: D48h-1,D48h-2,D48h-3.txt


title: miRNA AC2

value: liver

value: water week 22


title: miRNA AC1


title: acute lymphoblastic leukemia M19

value: acute lymphoblastic leukemia


title: acute lymphoblastic leukemia M18


title: Diploid jujube under 12h drought treatment (repeat 3)

description:
D12h-3
D12h-3_ZiziphusjujubaMill_V198-01-T15
processed data file: D12h-1,D12h-2,D12h-3.txt

value: 12h drought treatment


title: Mouse,Sham-circSCMH1,rep3


title: Diploid jujube under 12h drought treatment (repeat 2)

description:
D12h-2
D12h-2_ZiziphusjujubaMill_V198-01-T14
processed data file: D12h-1,D12h-2,D12h-3.txt


title: acute lymphoblastic leukemia M17


title: Diploid jujube under 12h drought treatment (repeat 1)

description:
D12h-1
D12h-1_ZiziphusjujubaMill_V198-01-T13
processed data file: D12h-1,D12h-2,D12h-3.txt


title: Mouse,Sham-circSCMH1,rep2


title: acute lymphoblastic leukemia M16


title: acute lymphoblastic leukemia M15


title: Diploid jujube under 6h drought treatment (repeat 3)

description:
D6h-3
D6h-3_ZiziphusjujubaMill_V198-01-T09
processed data file: D6h-1,D6h-2,D6h-3.txt


title: Mouse,Sham-Vector,rep3


title: Mouse,Sham-circSCMH1,rep1


title: Diploid jujube under 6h drought treatment (repeat 1)

description:
D6h-1
D6h-1_ZiziphusjujubaMill_V198-01-T07
processed data file: D6h-1,D6h-2,D6h-3.txt


title: Diploid jujube under 6h drought treatment (repeat 2)

description:
D6h-2
D6h-2_ZiziphusjujubaMill_V198-01-T08
processed data file: D6h-1,D6h-2,D6h-3.txt


title: acute lymphoblastic leukemia M13


title: acute lymphoblastic leukemia M20


title: acute lymphoblastic leukemia M14


title: acute lymphoblastic leukemia M12


title: Mouse,Sham-Vector,rep2


title: male parasites, klf4 RNAi, scRNAseq, rep1

data_processing:
Illumina Casava1.9 software used for basecalling.
Illumina bcl files were further processed using Cell Ranger (10x Genomics) according to the manufacturer's protocol
Outputs from Cell Ranger were analyzed using Seurat (v4.3)
Assembly: Schistosoma mansoni v7
Supplementary files format and content: R object (.rds) of combined dataset that was used to perform clustering

source_name: whole adult male parasites

extract_protocol:
100 male worms from each group were suspended in a 0.5% solution of Trypsin/EDTA (Sigma T4174) in PBS before rinsing in PBS for triple times. The worms were then triturated for approximately 10 minutes at room temperature until the solution became turbid and no large pieces of worms were left. The trypsin was inactivated by adding an equal volume of Basch media. The dissociated worms were then centrifuged at 500 g for 10 min at 4°C. Next the worms were resuspended in 1 ml of Basch medium followed by filtering through 100uM cell strainer to remove big chunks. The filtered collections were treated with 10 μL of RQ1 DNAse (Promega M6101) and incubated for 10 minutes at RT. After adding 3mL PBS, the dissociated worms were centrifuged again at 500 g for 10 minutes at 4°C. The cells were then resuspended in 1mL of staining media (0.2% BSA, 2mM EDTA in PBS, pH 7.40) and incubated in Hoechst 33342 (18 μg/ml) (Sigma B2261) for 30min at RT in the dark. The worms were centrifuged once again at 500 g for 10 minutes at 4°C. Worms were then resuspended in 1mL of staining media containing Hoechst 33342 (18 μg/ml) and propidium iodide (1 μg/ml) (Sigma-Aldrich P4170) and then filtered through a 100 μm cell strainer into a 12x75mm FACS tube prior to sorting. Filtered cells were then sorted on a FACSAria II custom (BD Biosystems) with 305/405/488/561/633nm lasers. Live single cells (PI negative, singlet by comparing forward scatter height to forward scatter width) were sorted using a 100 μm nozzle and cells were sorted into sorting media (0.2% BSA in PBS, pH 7.4). A Hoechst threshold was applied to exclude debris and improve the efficiency of sorting.
single-cell RNAseq libraries were prepared using a 10x genomics Chromium Controller according to the manufacturer's protocol

value: whole adult male parasites

value: Puerto Rico

value: klf4 dsRNA


title: Mouse,Sham-Vector,rep1

value: brain

value: photothrombotic (PT) stroke model treated with RVG-EVs


title: Diploid jujube under control environment (repeat 3)

description:
DCK-3
DCK-3_ZiziphusjujubaMill_V198-01-T03
processed data file: DCK-1,DCK-2,DCK-3.txt

value: leaves

value: after tissue culture of 30 days, well-growing plants were cultured in the rooting medium for 45 days

value: control environment


title: Diploid jujube under control environment (repeat 2)

description:
DCK-2
DCK-2_ZiziphusjujubaMill_V198-01-T02
processed data file: DCK-1,DCK-2,DCK-3.txt


title: acute lymphoblastic leukemia M11

source_name: blast cells, bone marrow


title: Mouse,PT-Vector,rep1


title: male parasites, control RNAi, scRNAseq, rep1

value: control dsRNA


title: acute lymphoblastic leukemia M10


title: Diploid jujube under control environment (repeat 1)

description:
DCK-1
DCK-1_ZiziphusjujubaMill_V198-01-T01
processed data file: DCK-1,DCK-2,DCK-3.txt


title: PS2KO5

city: Bonn

first: Ulrich

last: Schweizer

state: NRW

address: Nussallee 11

department: Institut für Biochemie und Molekularbiologie

country: Germany

institute: Universitätsklinikum Bonn

data_processing:
Sequence reads were trimmed with bbduk.sh following manufacturer's protocol. ref=/data/resources/polyA.fa.gz,/data/resources/truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=t trimq=10 minlength=20
Reads were aligned with STAR aligner following the manufacturer's protocol. STAR  --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1   --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20   --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD  --outSAMtype BAM SortedByCoordinate --outFileNamePrefix
Numbers of sequences aligned to transcripts were counted with STAR aligner
Assembly: GRCm38.104
Supplementary files format and content: raw counts for each Sample; table with 2 columns in .tab format, column1: Ensemble Gene Accession Number, column2: corresponding counts

source_name: MEF

growth_protocol: Mouse primary embryonic fibroblasts, WT, Psen1-KO, Psen2-KO cells

extract_protocol:
RNA: total RNA was extracted using TRIzol Reagent (Invitrogen) recommended by manufacturer.
Libraries were prepared with the QuantSeq 3’ mRNA-Seq Fw. Library Prep Kit (Lexogen) and sequenced to 10M raw reads on an Illumina HiSeq 2500 machine, following the manufacturer’s protocols.

value: MEF

tag: passage


title: acute lymphoblastic leukemia M9


title: acute lymphoblastic leukemia M8


title: PS2KO4


title: acute lymphoblastic leukemia M7


title: PS2KO3


title: NC72A

city: Riverside

first: Manuela

last: Martins-Green

address: 900 University Ave

institute: University of California, Riverside

data_processing:
Quality control was processed using Fastqc. Low quality reads were trimmed using trim_galore and high quality trimmed reads were aligned to the RPA reference genome using the STAR aligner. QC data were summarized using MultiQC. Fastq-screen was used to sample each library (1 M reads) and quickly align them to known references including humans, mouse, E. coli, Arabidopsis, vectors, adapters, etc. Sortmerna was used to determine the extent of the rRNA contamination within each library. Featurecount quantified the mapped reads with a genome annotation to generate a count matrix for each transcript/gene. A differential expression analysis was performed using DESeq2.
Assembly: PRJNA1112363
Supplementary files format and content: tab delineated text file contains raw counts for each sample

organism: Pseudomonas aeruginosa

source_name: nonchronic wound

growth_protocol: P. aeruginosa was grown in LB and inoculated into clean db/db wounds

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit, treated with Dnase, and cleaned with vacuum grease and isopropyl alcohol
Ribosomal transcripts were removed using the Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus and barcoded with IDT® for Illumina® RNA UD Indexes Set A Li-gation

treatment_protocol: chronic wounds were treated with inhibitors for antioxidant enzymes, catalase and GPx

value: nonchronic wound

value: prokaryote

tag: biological replicate

value: A


title: PS2KO2

tag: cell type


title: NC48B

value: B


title: PS2KO1

tag: genotype


title: acute lymphoblastic leukemia M6


title: NC48C

tag: tissue

value: C


title: circRNA AX6

value: liver

value: PTH week 22


title: acute lymphoblastic leukemia M4

value: acute lymphoblastic leukemia


title: acute lymphoblastic leukemia M5


title: circRNA AX7


title: circRNA AX8


title: NC48A


title: NC24C


title: acute lymphoblastic leukemia M3


title: circRNA AX2


title: circRNA AX3


title: NC24B


title: PS1KO3


title: NC24A


title: NC72C


title: NC72B


title: circRNA AX1


title: acute lymphoblastic leukemia M2


title: PS1KO2


title: circRNA AT8

value: CCL4 week 22


title: CW72C

source_name: chronic wound

value: chronic wound


title: PS1KO1


title: IAA+DSS rep4

first: Mengfan

address: 154 Anshan Road, Heping District, Tianjin

institute: Tianjin Medical University General Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

source_name: colon

extract_protocol:
Colon tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon

value: wild type


title: circRNA AT7


title: WT5

value: WT


title: PS1KO5


title: WT4


title: CW72B


title: WT7


title: acute lymphoblastic leukemia M1


title: IAA+DSS rep3


title: PS1KO4


title: CW48A


title: circRNA AT5


title: CW72A


title: WT3


title: CW24C


title: WT2


title: circRNA AT4


title: IAA+DSS rep2


title: WT6


title: CW48C


title: circRNA AT2


title: CW48B


title: IAA+DSS rep1


title: circRNA AT1


title: CW24A


title: vehicle+IAA rep3


title: Mi_L1_rep2

status: Public on May 25 2024

city: Wuhan

first: Dadong

last: Dai

state: Hubei

address: 1st street Shizishan

department: Department of Life science and technology

institute: Huazhong Agricultural University

data_processing:
sequence read was trimmed for adaptor sequence/low-quality using fastp (v0.20.1) software
read count extraction and normalization were performed using RSEM29 (v1.2.28)
Assembly: The genome used in this study was sequenced and assembled in our own laboratory and has not yet been published.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Meloidogyne incognita

source_name: whole organism

extract_protocol:
RNA was harvested by treating eggs with lysis buffer. Details can refer to smart-seq2 peotocols.
RNA libraries for RNA-seq were prepared using Smart-seq2 protocols.

value: whole organism


title: vehicle+IAA rep2


title: Mi_L1_rep3


title: Mi_L1_rep4


title: circRNA AC8

value: water week 22


title: Mi_L1_rep1


title: Mi_Moving_rep5


title: circRNA AC5


title: CW24B


title: Mi_Moving_rep3


title: Mi_2-fold_rep4


title: Mi_2-fold_rep2


title: Mi_2-fold_rep1


title: WT1


title: Mi_2-fold_rep5


title: vehicle+IAA rep1


title: Mi_1.5-fold_rep4


title: Mi_1.5-fold_rep5


title: Mi_L1_rep5


title: Mi_1.5-fold_rep3


title: vehicle+IAA rep4


title: circRNA AC1


title: Mi_Moving_rep2


title: Mi_Moving_rep4


title: Mi_Moving_rep1


title: Mi_1.5-fold_rep2


title: Mi_2-fold_rep3


title: Mi_1.5-fold_rep1


title: Mi_64-78cell_rep3


title: Mi_Comma_rep3


title: Mi_64-78cell_rep4


title: Mi_Comma_rep2


title: Mi_64-78cell_rep2


title: Mi_24-44cell_rep3


title: Mi_Comma_rep5


title: Mi_Comma_rep4


title: Mi_64-78cell_rep1


title: Mi_8-cell_rep2


title: Mi_24-44cell_rep5


title: Mi_4-cell_rep5


title: Mi_24-44cell_rep4


title: Mi_Comma_rep1


title: Mi_24-44cell_rep1


title: Mi_24-44cell_rep2


title: Mi_8-cell_rep4


title: Mi_8-cell_rep3


title: Mi_4-cell_rep4


title: Mi_4-cell_rep3


title: Mi_4-cell_rep2


title: Mouse 1, LN, Day 8 IP, CSP

city: Cambridge

first: James

last: Thaventhiran

address: Tennis Court Road

country: United Kingdom

institute: MRC Toxicology Unit

description: 10X Genomics

data_processing:
Raw FASTQ files of the gene expression library were analysed using 10x Genomics Cell Ranger software.
Generated count matrices were analyzed using Seurat and Scanpy (demultiplexing, quality control, normalization, clustering and differential gene expression)
Assembly: mm10
Supplementary files format and content: Comma-separated/ tab-separated values files, matrix and annotated data matrix files.

source_name: Lymph nodes

extract_protocol:
Freshly collected cells were sorted into PBS containing 10%FCS and 2mM EDTA in cold and spun down at 300g 7minutes 4°C before resuspension in PBS.
Single-cell RNA-seq libraries were prepared using Chromium Single Cell and V(D)J Enrichment Kits following the Single-Cell V(D)J Reagent Kits User Guide (Manual Part CG000086 Rev H, I, J, K, L, M; 10X Genomics). The data from the experiment using intraperitoneal tamoxifen were generated using chemistry (5’ v 1) before the introduction of dual-indexing strategy; the data for the intratumoural experiment was generated using chemistry (5’ v 2).

value: Lymph nodes

value: EYFP+ T cells

value: 8 days after intraperitoneal tamoxifen

tag: library type

value: scRNA-seq HTO


title: Mi_8-cell_rep1


title: Mi_Zygote_rep4


title: Mi_Zygote_rep3


title: Mouse 7, Tumour, Day 8 IP, VDJ

description: 10X Genomics

source_name: Tumour

value: Tumour

tag: treatment

value: scRNA-seq TCR


title: Mi_4-cell_rep1


title: Mi_Zygote_rep2


title: Mi_2-cell_rep5


title: Mi_2-cell_rep4


title: Mouse 7, Spleen, Day 8 IP, VDJ

description: 10X Genomics

source_name: Spleen

value: Spleen


title: Mi_2-cell_rep3


title: Mouse 2, LN, Day 8 IP, CSP

description: 10X Genomics


title: Mi_2-cell_rep1


title: Mouse 4, LN, Day 18 IP, CSP

description: 10X Genomics

value: 18 days after intraperitoneal tamoxifen


title: Mi_2-cell_rep2


title: Mi_Zygote_rep5


title: Hg_L1_rep5

organism: Heterodera glycines


title: Mi_Zygote_rep1


title: Mi_8-cell_rep5


title: Hg_L1_rep3


title: Mouse 6, Spleen, Day 18 IP, VDJ

description: 10X Genomics


title: Mouse 4, LN, Day 18 IP, VDJ

description: 10X Genomics


title: Hg_L1_rep2


title: Mouse 5, Spleen, Day 18 IP, VDJ

description: 10X Genomics


title: Mouse 4, Spleen, Day 18 IP, VDJ

description: 10X Genomics


title: Hg_L1_rep4


title: Hg_Moving_rep5


title: Mouse 2, LN, Day 8 IP, VDJ

description: 10X Genomics


title: Mouse 5, Tumour, Day 18 IP, VDJ

description: 10X Genomics


title: Mouse 2, Spleen, Day 8 IP, VDJ

description: 10X Genomics


title: Hg_Moving_rep1


title: Mouse 1, Spleen, Day 8 IP, VDJ

description: 10X Genomics


title: Hg_2-fold_rep1


title: Hg_2-fold_rep2


title: Hg_1.5-fold_rep4


title: Mouse 7, Spleen, Day 8 IP, GEX

description: 10X Genomics

value: scRNA-seq GEX


title: Mouse 6, Spleen, Day 18 IP, GEX

description: 10X Genomics


title: Hg_2-fold_rep4


title: Mouse 4, Tumour, Day 18 IP, VDJ

description: 10X Genomics


title: Hg_1.5-fold_rep2


title: Hg_2-fold_rep3


title: Hg_L1_rep1


title: Mouse 3, Tumour, Day 8 IP, VDJ

description: 10X Genomics


title: Hg_1.5-fold_rep3


title: Hg_Moving_rep4


title: Hg_1.5-fold_rep1


title: Hg_Moving_rep3


title: Hg_Moving_rep2


title: Mouse 6, Tumour, Day 18 IP, VDJ

description: 10X Genomics


title: Hg_Comma_rep3


title: Mouse 4, Tumour, Day 18 IP, GEX

description: 10X Genomics


title: Mouse 2, Tumour, Day 8 IP, VDJ

description: 10X Genomics


title: Mouse 1, LN, Day 8 IP, VDJ

description: 10X Genomics


title: Mouse 2, LN, Day 8 IP, GEX

description: 10X Genomics


title: Mouse 1, Tumour, Day 8 IP, VDJ

description: 10X Genomics


title: Hg_1.5-fold_rep5


title: Mouse 2, Tumour, Day 8 IP, GEX

description: 10X Genomics


title: Hg_64-78cell_rep3


title: Hg_64-78cell_rep2


title: Mouse 7, Tumour, Day 8 IP, GEX

description: 10X Genomics


title: Mouse 3, Spleen, Day 8 IP, VDJ

description: 10X Genomics


title: Mouse 5, Spleen, Day 18 IP, GEX

description: 10X Genomics


title: Mouse 6, Tumour, Day 18 IP, GEX

description: 10X Genomics


title: Mouse 5, Tumour, Day 18 IP, GEX

description: 10X Genomics


title: Mouse 4, LN, Day 18 IP, GEX

description: 10X Genomics


title: Hg_24-44cell_rep5


title: Hg_Comma_rep4


title: Mouse 4, Spleen, Day 18 IP, GEX

description: 10X Genomics


title: Mouse 1, Spleen, Day 8 IP, GEX

description: 10X Genomics


title: Hg_24-44cell_rep4


title: Mouse 1, Tumour, Day 8 IP, GEX

description: 10X Genomics


title: Hg_Comma_rep2


title: Hg_64-78cell_rep5


title: RNA0000948

city: Brussels

first: clement

last: triaille

address: avenue hippocrate

country: Belgium

institute: UCLouvain

data_processing:
Data were processed using a standard RNAseq analysis pipeline includingFastQC-0.11.8for quality control of raw data, andTrimmomatic-0.38to remove low quality reads and trim adapters from sequences.
Hisat2-2.1.0was used to align reads to the genome (GRCh38)
Gene expression levels were evaluated using featureCounts from subread-2.0.0  and Homo_sapiens.GRCh38.94.gtf.
Assembly: (GRCh38)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: bulk synovial tissue

extract_protocol:
Total RNA was extracted from synovial biopsies using the NucleoSpin RNA II extraction kit (Macherey-Nagel) including DNAse treatment. RNA quality control was performed on a 2100 Bioanalyzer (Agilent). RNASeq was performed on 350 ng of RNA, for  samples that yielded a RNA Integrity Number (RIN) of 5 or more
Sequencing was performed by Macrogen Europe using a standardized protocol. cDNA libraries were constructed with the TruSeq Stranded mRNA LT Sample Prep Kit and sequenced on an Illumina sequencer.

treatment_protocol: Synovial tissue biopsies were obtained in a clinically involved joint of JIA patients. Three to five synovial fragments were obtained from each joint by needle arthroscopy or US guided small joint biopsy and stored at -80°C after overnight incubation in RNA-Later solution (Invitrogen)

value: bulk synovial tissue

tag: rin

tag: antinuclear antibody

value: N

tag: subtype (oa_

tag: ongoing dmard_at_biopsy

tag: age at_biopsy_(years)


title: Mouse 3, Spleen, Day 8 IP, GEX

description: 10X Genomics


title: Hg_64-78cell_rep4


title: Mouse 3, Tumour, Day 8 IP, GEX

description: 10X Genomics


title: Hg_24-44cell_rep3


title: RNA0000826

value: Y


title: Hg_Comma_rep1


title: Mouse 2, Spleen, Day 8 IP, GEX

description: 10X Genomics


title: Hg_Comma_rep5


title: Mouse 1, LN, Day 8 IP, GEX

description: 10X Genomics


title: Hg_8-cell_rep5


title: Hg_8-cell_rep3


title: RNA0000813


title: Hg_64-78cell_rep1


title: Hg_24-44cell_rep2


title: RNA0000825


title: Hg_4-cell_rep5


title: RNA0000807


title: Hg_24-44cell_rep1


title: RNA0000814


title: RNA0000792


title: Hg_8-cell_rep4


title: Hg_4-cell_rep3


title: RNA0000806


title: Hg_4-cell_rep2


title: Hg_4-cell_rep4


title: RNA0000790


title: RNA0000778


title: Hg_8-cell_rep2


title: Hg_8-cell_rep1


title: RNA0000811


title: RNA0000777


title: RNA0000947


title: RNA0000808


title: RNA0000789


title: Hg_4-cell_rep1


title: Hg_2-cell_rep3


title: Hg_2-cell_rep2


title: RNA0000776


title: RNA0000775


title: Hg_Zygote_rep5


title: RNA0000791


title: Hg_Zygote_rep4


title: Hg_2-cell_rep1


title: 176539


title: RNA0000774


title: Hg_Zygote_rep3


title: Hg_2-cell_rep5


title: Hg_Zygote_rep2


title: Hg_2-cell_rep4


title: Hg_Zygote_rep1


title: LKB1 KO3

city: Nice

first: Corine

last: Bertolotto

address: 151 route Saint-Antoine de Ginestière

country: France

institute: C3M - U1065 INSERM - CENTRE MEDITERRANEEN DE MEDECINE MOLECULAIRE

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Assembly: hg38

source_name: 3 KO cell lines for LKB1

extract_protocol:
RNA extraction with trizol
RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: KO

tag: cell line background

value: metastasis-derived cell line (liver) that harbors a 626 A>C mutation in GNAQ Q209P


title: 205576


title: LKB1 KO1


title: Wild-type_24_3

city: Jena

first: Matthew

middle: George

last: Blango

address: Adolf-Reichwein-Str. 23

department: Junior Resaerch Group RNA Biology of Fungal Infections

institute: Leibniz Institute for Natural Product Research and Infection Biology

description:
50-bp single read sequencing at 10M reads
CEA17_24h_R3

data_processing:
*library strategy: tRF&tiRNA-seq
The sequencing results were analyzed with Unitas (https://doi.org/10.1186/s12864-017-4031-9) using default parameters.
A. fumigatus nuclear tRNAs were referenced from GtRNAdb, mitochondrial tRNAs were scanned from the mitochondrial genome using the 27 tRNAs predicted by tRNAscan-SE. All analyses were performed using “R” version 4.3.1 (2023-06-16) and Rstudio (2022-02-02), an integrated development environment (IDE) for R.
Assembly: Aspergillus fumigatus A1163 ASM15014v1
Supplementary files format and content: A single csv file (tiRNA_processed) contains the abundance of each target from each sample replicate.

organism: Aspergillus fumigatus

source_name: mycelium

growth_protocol: A. fumigatus was grown on Aspergillus minimal medium (AMM) agar plates (70 mM NaNO3, 11.2 mM KH2PO4, 7 mM KCl, 2 mM MgSO4, 1% (w/v) glucose and 1 μl/ml trace element solution (pH 6.5)). The trace element solution was composed of 1 g FeSO4 • 7 H2O, 8.8 g ZnSO4 • 7 H2O, 0.4 g CuSO4 • 5 H2O, 0.15 g MnSO4 • H2O, 0.1 g NaB4O7 • 10 H2O, 0.05 g (NH4)6Mo7O24 • 4 H2O, and ultra-filtrated water to 1000 ml. Spores were harvested after 5 days with 10 ml of sterile distilled water using a T-shaped inoculation spreader and spore suspensions were filtered through a 30-µm cell strainer (MACS, Miltenyi Biotec GmbH, Germany) to exclude mycelium.

extract_protocol:
Total RNA was isolated from three biological replicates of CEA17ΔakuBKU80 from conidia, 24-h-, and 48-h-old mycelium. For A. fumigatus conidia, the spores were first homogenized in a bead beater (0.5 mm beads; FastPrep-24, MP Biomedicals) in Trizol. Fungal mycelium was collected from liquid culture using Miracloth (Millipore) and disrupted in liquid nitrogen using a precooled mortar and pestle. Roughly 0.5 g of homogenized mycelium was transferred into a 2-ml Eppendorf tube. 800 µl TRIzol was added to the ground mycelia and vortexed vigorously. Tubes were frozen briefly for 5 sec in liquid nitrogen and allowed to thaw on ice. To all samples, chloroform was added to the fungal samples in TRIzol, vortexed, and centrifugated for 5 min at 4°C at full speed. The aqueous upper phase was transferred to a fresh 2-ml tube without disturbing the interphase. RNA extraction from aqueous phase was done with 1 volume of phenol/chloroform/isoamyl alcohol (25:24:1, v/v). Brief vortexing preceded centrifugation for 5 min at 4°C. RNA was precipitated using 400 µl isopropanol for 20 min, followed by pelleting by centrifugation for 20 min at 4°C. The pellet was washed with 700 µl 70% ethanol and air dried at 37°C for 5 min prior to resuspension in RNase free water. The RNA isolation was followed by a DNase treatment using 2 units of TURBO DNase (Thermo Fisher) per 10 µg RNA for 30 min at 37°C in 100 µl total volume. Total RNA was then collected using the RNA Clean and Concentrator-25 kit (Zymo Research) according to the manufacturer’s instructions.
tRF&tiRNA-seq (CD Genomics)
The following treatments were performed before library preparation for total RNA samples: 3’-aminoacyl (charged) deacylation to 3’-OH for 3’ adaptor ligation, 3’-cP (2’,3’-cyclic phosphate) removal to 3’-OH for 3’ adaptor ligation, 5’-OH (hydroxyl group) phosphorylation to 5’-P for 5’-adaptor ligation, m1A and m3C demethylation for efficient reverse transcription. Sequencing libraries were size-selectedfor the RNA biotypes to be sequenced using an automated gel cutter.The libraries were qualified and absolutely quantified using Agilent BioAnalyzer2100.

value: mycelium

value: CEA17 delta_akuB::KU80

tag: growth condition

value: Aspergillus minimal media

value: wild type

tag: time


title: Wild-type_48_1

description:
50-bp single read sequencing at 10M reads
CEA17_48h_R1


title: Wild-type_48_3

description:
50-bp single read sequencing at 10M reads
CEA17_48h_R3


title: Ctl2

source_name: 3 cell lines control

value: control


title: Wild-type_24_2

description:
50-bp single read sequencing at 10M reads
CEA17_24h_R2


title: Ctl1


title: Wild-type_24_1

description:
50-bp single read sequencing at 10M reads
CEA17_24h_R1


title: RNA0000496


title: Ctl3


title: Wild-type_conidia_3

description:
50-bp single read sequencing at 10M reads
CEA17_conidia_R3

source_name: conidia

value: conidia

value: Aspergillus minimal media agar plates

value: 0 h


title: Sister, biol rep 2

city: New Delhi

first: Vibha

last: Taneja

state: Delhi

address: Rajinder Nagar

department: Research

country: India

institute: Sir Ganga Ram Hospital

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimgalore (Phred score threshold of 20)
Trimmed sequence reads were mapped to GRCh38 using STAR aligner.
Read count extraction was done using Salmon and normalization were performed using Voom.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Blood

extract_protocol:
Peripheral blood was drawn in EDTA vials. Peripheral blood mononuclear cells (PBMCs) were separated by density gradient centrifugation on Histopaque-1077. RNA was isolated from PBMCs using RNAzol according to the manufacturer’s protocol
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Blood

value: Peripheral blood mononuclear cells

value: Juvenile Amyotrophic Lateral Sclerosis


title: Wild-type_conidia_2

description:
50-bp single read sequencing at 10M reads
CEA17_conidia_R2


title: RNA0000020


title: RNA0000027


title: Father, biol rep 2


title: Wild-type_conidia_1

description:
50-bp single read sequencing at 10M reads
CEA17_conidia_R1


title: Control, biol rep 2

value: healthy control


title: Donor1_DissociatedCNScells

city: Chapel Hill

first: Edward

middle: Patrick

last: Browne

state: NC

address: 120 Mason Farm Road

institute: UNC-Chapel Hill

description: Isolated from post-mortem brain tissue of person with HIV

data_processing:
Fastq data demultiplexed with mkfastq command
Mapping and cell-barcode assignment with Cellranger (v7.0.2) count function. Cellranger count run with default settings
We inputted the Cellranger output file, raw_feature_bc_matrix, into the R package Seurat 4.3.0. First we filtered out cells with transcripts with fewer than 200 genes. Second, we filtered cells expressing more than 2500 genes that can be considered potential doublets cells. Third, we removed cells if the mitochondria genes account for more than 5% of the transcriptome. Last, we filtered out genes that are expressed by 3 or lower than 3 cells. For clustering, we used Seurat package for clustering analysis with default parameters64. In Seurat, Principal Component Analysis (PCA) was performed with the 2000 informative genes; cells were embedded in a K-nearest neighbor (KNN graph); projected onto two dimensions and assign clusters by Louvain clustering. Cell clusters were visualized in two-dimensional UMAP space.
Assembly: GRCh38 + HIV reference genome HXB2 generated with cellranger mkref function
Supplementary files format and content: Donor1_raw_feature_bc_matrix.tar.gz and Donor2_raw_feature_bc_matrix.tar.gz contain cell barcode, features, and count data from cellranger analysis

source_name: Brain

extract_protocol:
High quality brain cells were used to generate single cell RNA-seq libraries using the Chromium Next GEM Single Cell 3’ reagent dual index kit v3.1 following manufactures protocol (CG000315 • Rev E). Diluted cell suspensions (>90% viability) with a targeted recovery of 10000 cells were barcoded using GEM technology (Gel Beads-in-emulsion) in a chromium controller device.
Library preparation performed according to manufacturer's protocol. First-strand synthesis was performed within GEMs before droplet breaking and clean-up. cDNA was amplified for 11 cycles and cleaned up. Amplified cDNA was then fragmented, end-repaired, A-tailed, and ligated to Illumina sequencing adapters. Adapter PCR was performed with a dual-index strategy.
Dual-indexed libraries were sequenced by Illumina Nextseq 2000 with the following conditions: Read 1 - 28 cycles; Read 2 - 90 cycles; i7 - 10 cycles; i5 – 10 cycles.

treatment_protocol: Brain tissue pieces were rinsed with 1x HBSS, and meninges and blood vessels were removed. The tissue pieces were diced into 0.2 cm3 pieces, and treated with 0.25% trypsin–EDTA with 10 µg/ml DNase I in 1x HBSS and incubated at 37°C for 1 hour with agitation. After incubation, the enzymes were inactivated by adding 10% FBS (volume/volume). The digested tissue pieces were triturated with a 10 mL pipet 10 times followed by a 5 ml pipet 10 times. To ensure a single-cell suspension, the dissociated tissue solution was passed through a spinal needle using a 20-mL syringe. After tissue dissociation steps, the myelin debris layer was removed by 35% Percoll density gradient as described before (Grabert and McColl 2018). The single-cell suspension of CNS cells was then generated. The cells were resuspended in 5 ml of ACK lysis buffer for 10 min to further get rid of red blood cells. The cells were counted on countess II and hemocytometer, then the viable cells were determined by trypan blue exclusion assay. T cells were then depleted from the isolated CNS cells by CD3 positive selection. BrMCs were purified from the CD3+ T cell-depleted CNS population with CD11b MicroBeads (Cat#130-049-601, Miltenyi Biotec). An aliquot of T cell-depleted CNS cells or CD11b+ BrMCs (0.5-5 million) were rinsed with 1 x HBSS. Dead cell-depletion was performed (Cat#17899, Stemcell Technologies) and cell suspension was inspected with Trypan blue staining.

value: Brain

value: Dissociated brain cells, CD3-depleted

value: Cell suspension isolated from post-mortem brain tissue and depleted of CD3+ cells.


title: Donor2_PurifiedBrainMyeloidCells

value: Brain myeloid cells (brMCs)

value: Cell suspension isolated from post-mortem brain tissue and depleted of CD3+ cells, then positively selected for CD11b positive cells.


title: Mother, biol rep 2


title: Wild-type_48_2

description:
50-bp single read sequencing at 10M reads
CEA17_48h_R2

value: mycelium


title: LKB1 KO2

value: KO

value: metastasis-derived cell line (liver) that harbors a 626 A>C mutation in GNAQ Q209P


title: Mouse 3, dLN, Day 8 IT, EYFP-

description: SMARTer Mouse TCR α/β Profiling kit (Takara Bio USA)

data_processing:
Sequencing data were analysed and clonotypes were called using MiXCR v4.4.2 with recommended settings for SMARTer Mouse TCR α/β Profiling kit (analyze takara-mouse-rna-tcr-smarter).
Cells were grouped by their TCR β sequences, and the top 200 largest EYFP+ clonal populations (by frequency in the 10 tumour) from each mice were used for subsequent analysis. Sequences matching public repertoires were removed (Immune Epitope Database).
Assembly: mm10
Supplementary files format and content: Tab-separated values files

source_name: Draining lymph node

extract_protocol:
Freshly collected cells were sorted into Buffer RLT Plus buffer (Qiagen) with 20mM DTT. Lysate was vortexed for 1 min and stored at −80 °C for subsequent analysis. Total RNA was then extracted with RNeasy Plus Micro Kit as per manufacturers recommendations. RNA QC with Tapestation High Sensitivity RNA showed RIN values above 9.8 for all samples.
Samples were prepared withTakara SMARTer Mouse TCR alpha-beta Profiling Kit for 96 samples as per manufacturers recommendations.

value: Draining lymph node

value: EYFP- T cells

value: 8 days after intratumoral tamoxifen

value: Other


title: Control, biol rep 1


title: Sister, biol rep 1


title: Mouse 3, dLN, Day 8 IT, EYFP+

value: EYFP+ T cells


title: Mouse 3, Tumour, Day 8 IT, EYFP-

value: Tumour


title: Mouse 2, dLN, Day 8 IT, EYFP-


title: Mother, biol rep 1

value: Blood

value: Peripheral blood mononuclear cells


title: Father, biol rep 1

value: Juvenile Amyotrophic Lateral Sclerosis


title: Mouse 2, dLN, Day 8 IT, EYFP+


title: Mouse 3, Tumour, Day 8 IT, EYFP+